Table 3 BLAST parameters and options

(a) Parameters mentioned in the text and Box 2

   -M

Matrix

   -r

Reward for a nucleotide match (BLASTNonly)

   -q

Penalty for a nucleotide mismatch (BLASTNonly)

   -G

Cost to open a gap (zero invokes default behavior)

   -E

Cost to extend a gap (zero invokes default behavior)

   -F

Filter query sequence

   -W

Word size; default length is used if set to zero

   -z

Effective length of the database (use zero to get the real size)

   -e

Expectation value (E)

(b) Additional useful parameters

   -i

Name of the query file

   -m

Alignment viewing options, which include:

   0 Pairwise alignment

   1 Query-anchored showing identities

   2 Query-anchored, no identities

   7 XML output

   -o

Name of the BLAST report output file

   -f

Threshold for extending hits; default is used if set to zero

   -g

Perform gapped alignment (not available with TBLASTX)

   -Y

Effective length of the search space (use zero get the real size)

   -S

Query strands to search against the database (for BLAST [NX], and TBLASTX) 3 is both, 1 is top, 2 is bottom

   -T

Produce HTML output

   -y

Drop-off (X) for BLAST extensions, in bits (0.0 invokes default behavior)

   -Z

X drop-off value for final gapped alignment (in bits)